Table 1

Ortholog gene counts in Synorth

Count of human orthologs detected in fish

Source

Zebrafish

Fugu

Tetraodon

Stickleback

Medaka

Ensembl

One2one

7,790

8,429

7,784

8,903

8,639

One2many

6,144

6,285

7,718

5,868

5,307

Many2many

2,711

1,410

1,541

1,592

1,311

Apparent_one2one (out-paralogs)

197

192

181

175

238

Total

16,842

16,316

17,224

16,538

15,495

Ensembl + Option 1 (include exonAlign predictions)

26,695

20,529

20,460

23,070

21,269

Ensembl + Option 2 (exclude out-paralogs)

16,645

16,124

17,043

16,363

15,257

Ensembl + Option 1 + Option 2 (Synorth default set)

20,036

18,427

18,094

19,449

18,236

Counts for the different ortholog classes in the Ensembl ortholog set, the Synorth exon predictions, and out-paralogs that can be excluded via options on the Synorth preference page (Additional data file 2). Option 1 represents the inclusion of additional ortholog predictions from our exonAlign pipeline. Option 2 represents the exclusion of out-paralogs. The exonAlign ortholog prediction pipeline and the method used to exclude out-paralogs are described in Additional data file 1. The Ensembl ortholog set was extracted from Ensembl Compara version 49.

Dong et al. Genome Biology 2009 10:R86   doi:10.1186/gb-2009-10-8-r86